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| Status |
Public on Jan 17, 2022 |
| Title |
scRNA-seq of fin and body zebrafish melanocytes |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre-existing transcriptional programs in the cell of origin. Here, we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body, whereas the acral subtype arises on the palms of the hands, soles of the feet, or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL-driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs, indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes, compared to body melanocytes, revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL-driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults.
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| Overall design |
For this experiment we used our zebrafish transgenic model of Acral melanoma, which was generated by injecting Casper fish with MniCoopR-GFP, mitfa:hsCRKL, mitfa:hsGAB2, mitfa:hsTERT, mitfa:Cas9-mCherry;U6nf1a-gRNA, mitfa:Cas9-mCherry;U6-nf1b-gRNA. Fish were dissected to collect body skin and fins, digested using liberase, and then FACS sorted for GFP+ melanocytes and GFP- microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 months post-fertilization. This led to generation of 4 samples total, GFP+ body cells, GFP- body cells, GFP+ fin cells, GFP- fin cells. Data was then analyzed and pooled together, taking note of their sample origin.
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| Contributor(s) |
Weiss JM, Hunter MV, Ma Y, Xu T, Chaligné R, White RM |
| Citation(s) |
35355015 |
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| Submission date |
Aug 09, 2021 |
| Last update date |
Apr 22, 2022 |
| Contact name |
Joshua M Weiss |
| E-mail(s) |
jmw2015@med.cornell.edu
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| Organization name |
Memorial Sloan Kettering Cancer Center
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| Department |
Cancer Biology and Genetics
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| Lab |
White
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| Street address |
417 E 68th St
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platforms (1) |
| GPL24995 |
Illumina NovaSeq 6000 (Danio rerio) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA753151 |
| SRA |
SRP331755 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE181748_Pooled_counts_matrix.csv.gz |
49.3 Mb |
(ftp)(http) |
CSV |
| GSE181748_RAW.tar |
219.2 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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